You say you want to automate the process but the at the same time you say you want to run some commands. Other answers contain some command but if you want to have automation, checking out unison might be worth a try. It allows not only unidirectional syncing but also provides a way to keep 2 directories in sync on different machines.

There are several solutions... One way impacts how you'll approach it is where it should be initiated from.

From the Unix device, you should be able to mount a Windows file share and handle it like keeping local files synchronized. (Filenames with characters that Windows dislike might complicate it...)

You can also share the drive and mount it using NFS on Windows (It is in Services for Unix on XP, and an optional component in Vista and newer (might need specific editions, some alternatives are also available)). (Samba can also be used for a Windows file share if you do not want to install the NFS client on Windows)

Once that is set up, you can use tools like Unison and Rsync (or cp for simple cases) (if you do it from the Unix side) or SyncToy or similar tools (for the Windows side) as you would for local files.

scp (and the PuTTY-bundled equivalent pscp might be easier to secure, but need SSH keys set up to work automatically). curl also supports SCP and SFTP (mainly for fetching files) and might be useful for several other options as well.